Computational phylogeneticscomputational phylogenetics uses algorithms to assemble phylogenetic trees.
a phylogenetic tree is a branching diagram representing evolutionary relationships between taxa or biological molecules.
Phylogenetic trees
Hedges & Kumar 2009. Timetree of Life. Oxford University Press
depending on the input data and the algorithm used, trees can be rooted or unrooted.
Alpha BetaDelta Gamma Epsilon
Phylogenetic trees
Gamma
Delta
AlphaBeta
Epsilon
most recent common ancestor
depending on the input data and the algorithm used, trees can be scaled to time or not
Phylogenetic trees
1Mya
2Mya
3Mya
4Mya
5Mya
trees can be bifurcating or multifurcating.
Phylogenetic trees
Characters different types of traits can be used to infer phylogenies.
Phenotypical data
Molecular data
Morphological traitsPhysiological traitsCytological traitsBehavioural traits
Immunological techniquesProteines (amino acid sequences)DNA DNA-DNA hybridisation Restriction enzyme sites Nucleotide sequence comparisons
Characters
Friedman 2008. Nature 454: 209-212.
Characters morphological traits can be measured in both extant and extinct taxa.
10mm Friedman 2008. Nature 454: 209-212.
Characters cytogenetic traits include the number, size and morphology of the chromosomes, behavior in meiosis and total DNA content
Zeltnera exaltata
Zeltnera venusta
Zeltnera calycosa
Mansion & Zeltner 2004. Am. J. Botany 91: 2069-2086.
Characters behavioural characteristics can be used to build trees.
Elk – Cervus canadensis
Moose – Alces alces
Fallow deer – Dama dama
Cap et al. 2008 Cladistics 24: 917-932.
Characters behavioural characteristics can be used to build trees.
Elk – Cervus canadensis
Moose – Alces alces
Fallow deer – Dama dama
Cap et al. 2008 Cladistics 24: 917-932.
Characters in immunological taxonomy, antibody-antigen recognition is used to estimate relatedness.
species B antigens
species C antigens
species A antigens
species A antibodies
precipitation
precipitation+++
AB C
Characters trees can be build by comparing amino acid sequences for the same protein in different species.
1 2 3 4 5 6 7 8 9 10
11
12
40
41
42
43
44
45
46
47
48
49
50
Bacteria P L F D F A Y Q G F A R … K N F G L Y N E R V G
Yeast A L F D T A Y Q G F A T … K N A G M Y G E R V G
Alfaalfa P F F D S A Y Q G F A S … K N M G L Y G E R V G
Chicken P F F D S A Y Q G F A S … K N F G L Y N E R V G
Rat P F F D S A Y Q G F A S … K N F G L Y N E R V G
Horse P F F D S A Y Q G F A S … K N F G L Y N E R V G
Pig P F F D S A Y Q G F A S … K N F G L Y N E R V G
Human P F F D S A Y Q G F A S … K N F G L Y N E R V G
P=proline, A=alanine, L=leucine, F=tryptophan, D=aspartic acid, T=threonine, S=serine, K=lysine, N=asparagine, M=methionine, G=glycine, Y=tyrosine, E=glutamic acid, R=arginine, V=valine
amino acid sequence of aspartate transaminase
Characters DNA hybridisation techniques allow the comparison of a billion of nucleotides.
dissociate into single strands
dissociate into single strands
add to incubation mixture
isolate hybrid double strands
determine melting temperature
radioactivelabeling
Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments.
N
N
N
N
G
C
A
T
A
T
T
A
C
G
N
N
N
N
…
…
3’
5’
…
…
5’
3’
T
A
A A T C
G
N
N
N
N
…
…
3’
5’
N
N
N
N
G
C
…
…
5’
3’ A AT T
EcoRI
Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments.
EcoRI HindIII Hpa1 Bg/II XbaI SmaI EcoRI Hpa1 Bg/II XbaI SmaI
Characters comparing nucleotide sequences among species is the most precise way of inferring phylogenetic relationships.
April 2011: 135 440 924 sequences 126 551 501 141 bases
Characters since 1995, 180 organisms were sequenced genome-wide
Drosophila melanogaster Rattus norvegicus Caenorhabditis briggsae Apis mellifera Takifugu rubripes Canis familaris Oryza sativa Tetraodon nigroviridis
Ciona intestinalis Caenorhabdites elegans Arabidopsis thala Anopheles gambiae Mus musculus Pan troglodytes Gallus gallus Homo sapiens
Populus trichocarpa
Characters some types of DNA evolve faster than others.
Nuclear DNAMitochondrial DNAMicrosatellites • easy to isolate
• evolves at a faster rate
• e.g. CAACAACAA…• evolve at an even faster rate
Character coding continuous quantitative characters are often reverted into discrete ones, e.g. by gap coding.
a b c d
state 0 state 1 state 2
Inferring phylogenies different approaches exist for inferring phylogenies
Parsimony methodsDistance methodsMaximum likelihood methodsBayesian inference methods
Testing phylogenies specific hypotheses about trees, evolutionary models and clocks can be tested statistically.
Testing models, trees and clocksBootstrap, jackknife and permutation tests